ETV3L

ETS variant transcription factor 3 like, the group of ETS transcription factor family

Basic information

Region (hg38): 1:157092043-157112412

Links

ENSG00000253831 ∙ NCBI:440695 ∙ ∙ HGNC:33834 ∙ Uniprot:Q6ZN32 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ETV3L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETV3L gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			33	6	2	41
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	8	4

Variants in ETV3L

This is a list of pathogenic ClinVar variants found in the ETV3L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-157092692-T-A		not specified	Uncertain significance (Jan 21, 2025)
1-157092695-G-A		not specified	Uncertain significance (Oct 02, 2023)
1-157092698-G-T		not specified	Uncertain significance (Jan 30, 2024)
1-157092701-G-A		not specified	Uncertain significance (Oct 30, 2023)
1-157092706-G-C		not specified	Likely benign (Jan 03, 2024)
1-157092707-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-157092734-G-T		not specified	Uncertain significance (Apr 24, 2024)
1-157092802-T-C		ETV3L-related disorder	Likely benign (Dec 13, 2022)
1-157092815-G-A		not specified	Uncertain significance (May 05, 2023)
1-157092826-C-A		not specified	Uncertain significance (Sep 22, 2023)
1-157092839-C-T			Benign (Oct 13, 2017)
1-157092848-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-157092922-G-A			Likely benign (May 01, 2022)
1-157092944-G-A		ETV3L-related disorder	Likely benign (Jun 09, 2020)
1-157092996-G-A		not specified	Uncertain significance (Jan 24, 2025)
1-157093007-T-C		not specified	Uncertain significance (Mar 30, 2024)
1-157093032-G-C		not specified	Uncertain significance (Aug 26, 2024)
1-157093050-C-A		not specified	Likely benign (Dec 19, 2022)
1-157093052-C-T		not specified	Uncertain significance (Sep 28, 2022)
1-157093056-G-T		not specified	Uncertain significance (Jan 23, 2024)
1-157093067-T-A		not specified	Uncertain significance (Dec 28, 2022)
1-157093071-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-157093102-G-C		not specified	Uncertain significance (Dec 18, 2023)
1-157097868-G-A		ETV3L-related disorder	Likely benign (Dec 31, 2019)
1-157097873-A-T		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETV3L	protein_coding	protein_coding	ENST00000454449	5	7765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.20e-8	0.258	125640	0	106	125746	0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.348	217	203	1.07	0.0000114	2306
Missense in Polyphen		53	53.319	0.99402		635
Synonymous	-0.142	89	87.3	1.02	0.00000515	751
Loss of Function	0.427	12	13.7	0.875	8.56e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00335	0.00335
Ashkenazi Jewish	0.000419	0.000397
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator. {ECO:0000250}.

Intolerance Scores

• loftool: 0.772
• rvis_EVS: 1.44
• rvis_percentile_EVS: 95.08

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Etv3l

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;sequence-specific DNA binding